Your best bet if you want to unistall CC2 and only go with CC3 is to do the following:

UnInstall EVERYTHING from Profantasy (yeah, that means your CC3 and stuff right now), once everything is gone (make sure you keep your maps and stuff though )

Then follow the instructions at ProFantasy's site for installing CC3, DD3, CD3, the two symbol Sets, and the patches. After that, check and see if they have a CC3 upgrade patch for anything from CC2 you want to use with CC3.